First, I'd just like to say that I was so glad that Phoenix got his happy ending. I'd also like to say that your cover is very cute, though I would recommend changing the title to "Phoenix in the In-Between" because the word "is" just feels extra.
Read the story now
Here are a few picky little things: writing stuff is called "stationery" while something that is not moving is "stationary." A few times in your book you say Phoenix is ten, and a few times you say he's eleven going on twelve, so which is it? I also personally thought that letters 1-5 were quite repetitive and so you could either decrease the number of letters or find a little bit more plot to put into those first few.
There are a few things that need to be adjusted IF Phoenix is American, like the "President's House" being called the White House, no prefects in schools, no reserves on the soccer team, Phoenix's height being measured in feet and inches instead of centimeters, etc.
I thought it was a little strange that the letters were very letter-y until letter 7, where there starts to be more dialogue in the letters, which is kind of unrealistic for letters. I also thought that the letters to the fake doctor were a little bit of a weird way for Phoenix's parents to figure out how to understand him, and it honestly played into my thoughts about him being a rich kid before his dad became president, because it sounded exactly like something that rich people who didn't know how to talk to their own kid would do. Maybe set it up in the prologue so that Phoenix just feels he can't talk to his parents about these things so that the letters are more justified?
Anyway, I really liked how Phoenix didn't feel like he was weird for being trans, because I feel like that's how a lot of people get represented and I never thought it was quite fair. On a personal note, I'm not trans but I fought the battle against girly clothes and make up for my entire childhood, so I really related to Phoenix and, again, I'm just glad that he got his happy ending